BN1128 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.7453e-07 8.3087e-05
Layer 3 3.4448e-06 2.4631e-04
Layer 2 9.9903e-06 1.1881e-02
WM 1.5407e-05 1.3342e-01
Layer 5 2.2832e-05 7.9970e-04
Layer 6 3.1800e-04 1.0023e-02
Layer 1 5.6569e-01 5.2825e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
KCNA2 Expression Distribution
Gene Specificity Score (GSS)
KCNA2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
KCNA2 Layer 4 2.9375 0.7235
CHGA Layer 4 2.8652 0.7150
DIRAS1 Layer 4 2.8828 0.7121
SCN1B Layer 4 2.9277 0.7119
VAMP1 Layer 4 3.1533 0.7106
TUBB3 Layer 5 2.4512 0.7078
CPLX1 Layer 4 2.9922 0.7050
RPH3A Layer 4 2.8965 0.7035
SNCA Layer 5 2.3281 0.6965
SULT4A1 Layer 4 2.6865 0.6961
ELAVL2 Layer 5 2.8398 0.6949
PFKM Layer 4 2.8057 0.6947
CRYM Layer 5 2.8994 0.6930
INPP5F Layer 4 2.5215 0.6929
NUAK1 Layer 3 2.5664 0.6899
VDAC3 Layer 4 2.4395 0.6890
EPB41L1 Layer 4 2.5986 0.6884
CNTNAP1 Layer 4 2.4541 0.6881
APBA2 Layer 4 2.5508 0.6861
PHF24 Layer 5 2.5957 0.6859
TTC9B Layer 4 3.0781 0.6855
TUBB4B Layer 4 2.3574 0.6844
SH3GL2 Layer 4 2.5986 0.6827
CEND1 Layer 4 2.5664 0.6824
IQSEC1 Layer 4 2.5225 0.6822
IPCEF1 Layer 4 2.7852 0.6802
ATXN7L3 Layer 4 2.5244 0.6787
NSG1 Layer 3 2.4727 0.6786
GABRG2 Layer 4 2.7217 0.6776
PFKP Layer 5 2.6133 0.6767
SREBF2 Layer 3 2.2676 0.6766
TOLLIP Layer 4 2.2969 0.6757
KCNC2 Layer 4 3.0156 0.6757
RORB Layer 4 4.9883 0.6755
TRIM37 Layer 5 2.7129 0.6747
SNAP91 Layer 4 2.5273 0.6742
SCN1A Layer 4 3.2080 0.6734
GRAMD1B Layer 4 2.7217 0.6727
ACSL6 Layer 4 2.7598 0.6725
SNCG Layer 5 3.0859 0.6712
ATXN7L3B Layer 4 2.4180 0.6712
EPDR1 Layer 5 2.6543 0.6707
CAMK2G Layer 4 2.6016 0.6707
NRN1 Layer 5 2.5605 0.6706
KLHL7 Layer 4 2.3555 0.6705
SLC12A5 Layer 4 2.6367 0.6704
RAB3C Layer 5 2.7715 0.6704
SYT4 Layer 4 2.5781 0.6698
MAPK10 Layer 5 2.3867 0.6695
SYNGR1 Layer 4 2.7939 0.6681

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1128
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1128_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1128/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1128/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1128/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1128/report/PD/BN1128_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1128/report/PD/BN1128_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:22:01
  • Number of Processes: 10
  • Spending Time: 0h 4m